The avian corneal primary stroma has a unique structure. It consists of orthogonally arranged layers of collagen fibrils, composed of type I and II collagens that are produced by corneal epithelial cells. The primary stroma contains also type IX collagen, at least as a transitory component, and my recent studies show that the corneal form of this unique extracellular matrix molecule is different from that which is expressed in cartilage. Whereas cartilage type IX molecules contain a large globular amino-terminal domain located in the perifibrillar matrix along collagen fibrils, this domain is absent in corneal type IX collagen molecules. I propose that analysis of this difference will provide novel and exciting clues to answer the general question of what mechanisms cells utilize to build unique extracellular matrices in different tissues from a common set of extracellular matrix genes. As a first step in this analysis, DNA cloning and sequencing techniques will be applied to characterize the structure of corneal type IX collagen. In addition, rotary shadowing electron microscopy, western blotting and immunoprecipitation will be used to characterize the corneal type IX collagen protein. Second, the differential expression of the two different type IX collagens, the corneal and cartilage forms, will be examined by means of RNase protection methods in different tissues such as cornea, sclera, lens, retina, notochord, neural tube epithelium and cartilage. Third, to precisely locate the cells expressing the two forms of type IX collagen, in situ hybridization studies will be performed using DNA probes containing cornea and cartilage specific type IX collagen nucleotide sequences. Finally, the al(IX) gene will be examined in experiments aimed at deciphering the molecular mechanisms involved in expression of the corneal form of type IX collagen.